This invention relates generally to gene expression and in particular, to a method and polynucleotides for determining codon utilization in particular cells or tissues of an organism. More particularly, the method and polynucleotides of the invention are concerned with ascertaining codon preferences in cells or tissues for the purpose of modifying the translational efficiency of protein-encoding polynucleotides in those cells or tissues.
It is well known that a “triplet” codon of four possible nucleotide bases can exist in 64 variant forms. These forms provide the message for only 20 different amino acids (as well as translation initiation and termination) and this means that some amino acids can be encoded by more than one codon. Some amino acids have as many as six “redundant”, alternative codons while some others have a single, required codon.
For reasons not completely understood, codon utilization is highly biased in that alternative codons are not at all uniformly present in the endogenous DNA of differing cell types. In this regard, there appears to exist a variable natural hierarchy of “preference” for certain codons between different cell types or between different organisms.
Codon usage patterns have been shown to correlate with relative abundance of isoaccepting transfer RNA (iso-tRNA) species, and with genes encoding proteins of high versus low abundance. Moreover, the present inventors recently discovered that the intracellular abundance of different iso-tRNAs varies in different cells or tissues of a single multi-cellular organism (see copending International Application No. PCT/AU98/00530).
The implications of codon preference phenomena on gene expression are manifest in that these phenomena can affect the translational efficiency of messenger RNA (mRNA) It is widely known in this regard that translation of “rare codons”, for which the corresponding iso-tRNA is in relatively low abundance, may cause a ribosome to pause during translation which can lead to a failure to complete a nascent polypeptide chain and an uncoupling of transcription and translation.
A primary goal in recombinant research is to provide transgenic organisms with expression of a foreign gene in an amount sufficient to confer the desired phenotype to the organism. However, expression of the foreign gene may be severely impeded if a particular host cell of the organism or the organism itself has a low abundance of iso-tRNAs corresponding to one or more codons of the foreign gene. Accordingly, a major aim of investigators in this field is to first ascertain the codon preference for particular cells or tissues in which a foreign gene is to be expressed, and to subsequently alter the codon composition of the foreign gene for optimized expression in those cells or tissues.
Codon preference may be determined simply by analyzing the frequency at which codons are used by genes expressed in a particular cell or tissue or in a plurality of cells or tissues of a given organism. Codon frequency tables as well as suitable methods for determining frequency of codon usage in an organism are described, for example, in an article by Sharp et al (1988, Nucleic Acids Res. 16 8207-8211). The relative level of gene expression (e.g., detectable protein expression Vs no detectable protein expression) can provide an indirect measure of the relative abundance of specific iso-tRNAs expressed in different cells or tissues.
Alternatively, codon preference may be determined by measuring the relative intracellular abundance of different iso-tRNA species. For example, reference may be made to copending International Application No. PCT/AU98/00530 that describes a method that utilizes labeled oligonucleotides specific for different iso-tRNAs to probe an RNA extract prepared from a particular cell or tissue source.
The above methods provide useful indirect evidence for determining codon preference. However, such indirect evidence may not provide an accurate indication of the translational efficiency of a given codon. Accordingly, there is a need to provide a method that more directly ascertains the translational efficiency of a codon in a cell or tissue.